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  • Help is needed with openmpi and Ray on cluster

    Hi,

    I run a small Ray job on a cluster to check openmpi and Ray. The current versions on the cluster are openmpi-1.6.4 and Ray is 2.1.

    When compiled on my server with openmpi-1.4, Ray2.1 works just fine with large metazoan dataset (about 30 GB) completing assembly in about 20 hours on machine with 2 quad core E5620 (16 threads) and 96GB memory

    On the cluster Ray2.1 compiled fine as well, and then I tried to run it with one of datasets (about 36 MB) from the above pile that assembled fine on my server. It failed, generating ouput, which I am not quite understand and would appreciate help in interpretation and fixing the problem. Here is Ray.job file:

    Code:
    #$ -S /bin/bash
    #$ -cwd
    #
    #$ -N RayTest
    #$ -pe openmpi 32
    #$ -l h_rt=00:10:00,s_rt=00:08:00,h_vmem=3G
    #$ -j y
    #
    #$ -M [email protected]
    #$ -m eas
    #
    # Load the appropriate module files
    # Should be loaded already
    #$ -V
    
    mpiexec -n $NSLOTS ~/bin/Ray ~/jobs/Ray/Ray.conf
    Here is Ray.conf file:

    Code:
    # configuration file
    -k 31 # k-mer=31
    
    # default autocalc averageOuterDistance standardDeviation
    # all reads trimmed, Q30, FGMGPGIGVA
    
    -s <TestFile.fasta>                    # single read file
    
    -o ~/jobs/Ray/RayOutput         # outputDirectory
    
    -one-color-per-file                # Sets one color per file instead of one per sequence
    -amos                           # writes the AMOS file called RayOutput/AMOS.afg
    #-show-memory-usage              # Shows memory usage
    # -show-memory-allocations        # Shows memory allocation events
    #-write-checkpoints ~/SC/Ray/Checkpoints   # Write checkpoint files
    The ouput file is a bit loger, so it is attached.
    Attached Files

  • #2
    make options

    Did you specify your MPICXX during compile?

    make PREFIX=`pwd` MAXKMERLENGTH=99 MPICXX='/shared/openmpi/intel/bin/mpicxx'

    also I use mpirun -np numberofcpu

    Comment


    • #3
      [SOLVED] Help is needed with openmpi and Ray on cluster

      The cluster guys quickly pointed my error - I compiled Ray with an earlier existing version of openmpi before the latest version was installed on the cluster. I recompuiled it and all works fine now. Thanks to everyone who read my post and responded or was going to respond!

      Comment

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